individual_id linking from home sample list

[dnil]

This PR adds a functionality or fixes a bug.

How to test:

1. visit a case that loads nicely from scout-stage, go back to home page in gens and note that the link back to the case is broken on master
2. on this branch, rinse and repeat and note link working

As for the actions, note deprecation warnings missing from Checks.

Expected outcome: The functionality should be working Take a screenshot and attach or copy/paste the output.

Review:

• [ ] code approved by

[dnil]

Looks like connexion is not quite there yet with Flask 2.3 compatibility? They have a 2.0 in alpha, so likely soon, but we 🥶 for now. Scout is anyway also on the same freeze.

From stage:

May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     worker.init_process()
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/gunicorn/workers/base.py", line 134, in init_process
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     self.load_wsgi()
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/gunicorn/workers/base.py", line 146, in load_wsgi
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     self.wsgi = self.app.wsgi()
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/gunicorn/app/base.py", line 67, in wsgi
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     self.callable = self.load()
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/gunicorn/app/wsgiapp.py", line 58, in load
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     return self.load_wsgiapp()
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/gunicorn/app/wsgiapp.py", line 48, in load_wsgiapp
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     return util.import_app(self.app_uri)
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/gunicorn/util.py", line 359, in import_app
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     mod = importlib.import_module(module)
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/importlib/__init__.py", line 127, in import_module
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     return _bootstrap._gcd_import(name[level:], package, level)
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 991, in _find_and_load
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 961, in _find_and_load_unlocked
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 991, in _find_and_load
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap_external>", line 783, in exec_module
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/home/app/app/gens/__init__.py", line 2, in <module>
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     from .app import create_app
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/home/app/app/gens/app.py", line 9, in <module>
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     import connexion
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/connexion/__init__.py", line 32, in <module>
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     from .apps.flask_app import FlaskApp
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:   File "/usr/local/lib/python3.8/site-packages/connexion/apps/flask_app.py", line 151, in <module>
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]:     class FlaskJSONEncoder(json.JSONEncoder):
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]: AttributeError: module 'flask.json' has no attribute 'JSONEncoder'
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]: [2023-05-08 10:56:27 +0200] [4] [INFO] Worker exiting (pid: 4)
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]: [2023-05-08 10:56:27 +0200] [2] [INFO] Shutting down: Master
May 08 10:56:27 cg-vm1.scilifelab.se conmon[791284]: [2023-05-08 10:56:27 +0200] [2] [INFO] Reason: Worker failed to boot.

[dnil]

And ✅ on the tests! 😁

[dnil]

☑️ Deployed:

[hiseq.clinical@cg-prod-services ~]$ systemctl --user stop gens@latest; systemctl --user start gens@latest